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Kategorie/Name/Version (default)bio/structure/2.3.4
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LizenzFree Software
URL http://pritchardlab.stanford.edu/structure.html
What-isbio/structure/2.3.4 : STRUCTURE Command-Line-Version. SW package for using multi-locus genotype data to investigate population structure (command 'structure PATH_TO_MAINPARAMS-FILE')
Hilfe-Text
The program structure is a free software package for using multi-locus
  genotype data to investigate population structure. Its uses include
  inferring the presence of distinct populations, assigning individuals
  to populations, studying hybrid zones, identifying migrants and admixed
  individuals, and estimating population allele frequencies in situations
  where many individuals are migrants or admixed. It can be applied to
  most of the commonly-used genetic markers, including SNPS,
  microsatellites, RFLPs and AFLPs.

  In order to simplify batch runs and make it easier to run simulations 
  involving structure, the run-time version of Structure has added 
  command-line flags that update the values of certain parameters, 
  over-riding the values set in 'mainparams'.

  These are as follows:

  -m (mainparams) Read a different parameter input file instead of
     mainparams
  -e (extraparams) Read a different parameter input file instead of
     extraparams
  -s (stratparams) Read a different parameter input file instead of
     stratparams. (For use with the accompanying program, STRAT, 
     for association mapping.)
  -K (MAXPOPS) Change the number of populations.
  -L (NUMLOCI) Change the number of loci.  
  -N (NUMINDS) Change the number of individuals.
  -i (input file) Read data from a different input file.
  -o (output file) Print results to a different output file.
  -D (SEED) Initialize the random number generation using the value SEED. 
     Note that RANDOMIZE MUST be set to 0 to use this option.)

  Thus, to override one of the preset parameter values, we invoke structure
  and then use the relevant flag, followed by the new parameter value. 
  The flag and new value are separated by a space. The flags can be used 
  in any order.
  For example, to change the number of assumed populations to 5, and 
  direct the output to a file called output5, we could call structure
  as follows: ./structure -K 5 -o output5

  More documentation:

* http://pritchardlab.stanford.edu/structure_software/release_versions/v2.3.4/structure_doc.pdf
  /opt/bwhpc/common/bio/structure/2.3.4/console/structure_doc.pdf

In case of problems, please contact: bwhpc (at) uni-konstanz.de

           *** THIS IS THE COMMAND-LINE version ***

ATTENTION: We need at least a 'mainparams' and 'extraparams'-file
           in your current directory to get 'structure' started.
           Examples are found in: 
           /opt/bwhpc/common/bio/structure/2.3.4/console/mainparams
           /opt/bwhpc/common/bio/structure/2.3.4/console/extraparams
           /opt/bwhpc/common/bio/structure/2.3.4/bwhpc-examples/*

  and READ CAREFULLY!

           /opt/bwhpc/common/bio/structure/2.3.4/bwhpc-examples/README.bwhpc

This module is available for all users.
SupportbwHPC Support-Portal
Installationsdatum05.10.2017
Löschdatum
Best-Practice-Wikihttp://www.bwhpc-c5.de/wiki/index.php/Structure